Protein-metabolite interactomics of carbohydrate metabolism reveal regulation of lactate dehydrogenase

Metabolic networks are interconnected and influence diverse cellular processes. The protein-metabolite interactions that mediate these networks are frequently low affinity and challenging to systematically discover. We developed mass spectrometry integrated with equilibrium dialysis for the discover...

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Published inSCIENCE Vol. 379; no. 6636; pp. 996 - 1003
Main Authors Hicks, Kevin G., Cluntun, Ahmad A., Schubert, Heidi L., Hackett, Sean R., Berg, Jordan A., Leonard, Paul G., Ajalla Aleixo, Mariana A., Zhou, Youjia, Bott, Alex J., Salvatore, Sonia R., Chang, Fei, Blevins, Aubrie, Barta, Paige, Tilley, Samantha, Leifer, Aaron, Guzman, Andrea, Arok, Ajak, Fogarty, Sarah, Winter, Jacob M., Ahn, Hee-Chul, Allen, Karen N., Block, Samuel, Cardoso, Iara A., Ding, Jianping, Dreveny, Ingrid, Gasper, William C., Ho, Quinn, Matsuura, Atsushi, Palladino, Michael J., Prajapati, Sabin, Sun, Pengkai, Tittmann, Kai, Tolan, Dean R., Unterlass, Judith, VanDemark, Andrew P., Vander Heiden, Matthew G., Webb, Bradley A., Yun, Cai-Hong, Zhao, Pengkai, Wang, Bei, Schopfer, Francisco J., Hill, Christopher P., Nonato, Maria Cristina, Muller, Florian L., Cox, James E., Rutter, Jared
Format Journal Article Publication
LanguageEnglish
Published United States 10.03.2023
Subjects
Allosteric Regulation
Carbohydrate Metabolism
Fatty Acids - metabolism
Humans
L-Lactate Dehydrogenase - metabolism
Mass Spectrometry - methods
Metabolome
Organ Specificity
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Summary:Metabolic networks are interconnected and influence diverse cellular processes. The protein-metabolite interactions that mediate these networks are frequently low affinity and challenging to systematically discover. We developed mass spectrometry integrated with equilibrium dialysis for the discovery of allostery systematically (MIDAS) to identify such interactions. Analysis of 33 enzymes from human carbohydrate metabolism identified 830 protein-metabolite interactions, including known regulators, substrates, and products as well as previously unreported interactions. We functionally validated a subset of interactions, including the isoform-specific inhibition of lactate dehydrogenase by long-chain acyl–coenzyme A. Cell treatment with fatty acids caused a loss of pyruvate-lactate interconversion dependent on lactate dehydrogenase isoform expression. These protein-metabolite interactions may contribute to the dynamic, tissue-specific metabolic flexibility that enables growth and survival in an ever-changing nutrient environment. Understanding how metabolic state influences cellular processes requires systematic analysis of low-affinity interactions of metabolites with proteins. Hicks et al . describe a method called MIDAS (mass spectrometry integrated with equilibrium dialysis for the discovery of allostery systematically), which allowed them to probe such interactions for 33 enzymes of human carbohydrate metabolism and more than 400 metabolites. The authors detected many known and many new interactions, including regulation of lactate dehydrogenase by ATP and long-chain acyl coenzyme A, which may help to explain known physiological relations between fat and carbohydrate metabolism in different tissues. —LBR A mass spectrometry and dialysis method detects metabolite-protein interactions that help to control physiology.
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Present address: Brazilian Nanotechnology National Laboratory, Brazilian Center for Research in Energy and Materials, Campinas, Brazil.
Author contributions: H.-C.A., K.N.A., S.B., I.A.C., J. D., I.D., W.C.G., Q.H., A.M., M.J.P., S.P., P.S., K.T., D.R.T., J.U., A.P.V., M.G.V.H., B.A.W., C.-H.Y., and P.Z. are listed alphabetically in the author list. Conceptualization: K.G.H. and J.R. Methodology: K.G.H. and J.E.C. Software: J.A.B., S.R.H., Y.Z., and B.W. Validation: K.G.H., A.A.C., P.G.L., M.A.A.A., A.J.B., A.B., P.B., S.T., A.L., A.G., A.A., S.R.S., and F.J.S. Formal analysis: K.G.H., J.A.B., S.R.H., and A.J.B. Investigation: K.G.H., A.A.C., P.G.L., M.A.A.A., A.J.B., A.B., P.B., S.T., S.R.S., A.L., A.G., A.A., and J.M.W. Resources: H.L.S., M.A.A.A., H.-C.A., K. N.A., S.B., I.A.C., J.D., I.D., W.C.G., Q.H., A.M., M.J.P., S.P., P.S., K.T., D.R.T., J.U., A.P.V., M.G.V.H., B.A.W., C.-H.Y., P.Z., C.P.H., M.C.N., F.L.M., J.E.C., F.C., and F.J.S. Writing – original draft: J.R. and K.G.H. Writing – review & editing: J.R., K.G.H., S.F., A.A.C., P.G.L., M.A.A.A., S.T., J.M.W., I.A.C., M.G.V.H., M.C.N., J.E.C., and F.J.S. Visualization: K.G.H., A.A.C., J.A.B., Y.Z., A.J.B., J.M.W., A.B., P.B., S.T., A.L., A.G., A.A., S.R.S., F.J.S., and B.W. Supervision: J.R. and K.G.H. Project administration: J.R. and K.G.H. Funding acquisition: J.R. and K.G.H.
These authors contributed equally to this work.
Present address: Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA.
Present address: Skaggs Graduate School of Chemical and Biological Sciences, Scripps Research Institute, La Jolla, CA, USA.
Present address: College of Medicine, Baylor University, Houston, TX, USA.
ISSN:0036-8075
1095-9203
1095-9203
DOI:10.1126/science.abm3452